Solution plasma process (SPP) was used for sterilizing Staphylococcus aureus (S. aureus) in raw milk (RM). The sterilization efficacy analysis and kinetics analysis showed bacterial concentration and the distance between electrodes were negatively correlated with the sterilization effect, while discharge voltage was positive. The better sterilization effect was achieved at 4 kV. The electrochemical indices analysis indicated that pH value of RM had no changed. The DO content decreased. The conductivity increased with the increasing discharge voltage. The nutrient content analysis revealed that the content of acidity, lactose, fat, and protein decreased. RM after SPP treatment exhibited higher values of sourness and slightly lower values of astringency than the control. The higher discharge voltage and narrower distance between electrodes presented the stronger effect. The structural characterization of CMs and MFGs was carried out using a laser particle sizer, FTIR, 1H NMR, XRD, and AFM. The results showed that the main chemical structure of CMs was unchanged basically. The SPP with the narrower distance between electrodes and lower discharge voltage significantly reduced the size and aggregation of MFGs at the molecular level. At 4 kV/2 mm, the particle sizes of CMs and MFGs were reduced from 238 nm and 523 nm to 224 nm and 302 nm, respectively. The average diameter of MFGs was reduced from 45 nm to 18 nm. Therefore, SPP is a potential method in the milk industry and provides a new idea for the preservation and processing of beverage.